title: Fetal Forebrain Lib#2 RNA

first: Zhu

last: Chenxu

email: cxzhu@pku.edu.cn, czhu@nygenome.org

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Library strategy: Paired-seq
Cellular barcodes and the linker sequences are read by Read2. The first base of BC#1, BC#2, BC#3 and BC#4 should locate within 121-124th, 84-87th, 47-50th and 10-13rd base of read2
Nextera adaptor sequences were trimmed from 3’ of DNA libraries, Poly-dT sequences were trimmed from 3’ of RNA libraries and low-quality reads (length < 30, quality < 20) were excluded for further analysis.
Reads were first mapped to a reference genome using STAR (version: 2.6.0a) with the combined reference genome (GRCh37 for human and GRCm38 for mouse). Duplicates were removed based on the mapped position and UMI.
Genome_build: hg19/mm10
Supplementary_files_format_and_content: tab-delimited text files include cell embeddings for each cell.

source_name: Fetal Forebrain

growth_protocol: HEK293T (human), HepG2 (human) and NIH/3T3 (mouse) cells were cultured according to standard procedures in Dulbecco’s Modified Eagles’ Medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific) and 1% penicillin–streptomycin (Thermo Fisher Scientific) at 37 °C with 5% CO2.

extract_protocol:
Male C57BL/6J mice were purchased from Jackson laboratories at 8 weeks of age and maintained in the Salk animal barrier facility on 12 hr dark-light cycles with food ad libitum for four weeks before dissection. Cerebral cortex was dissected and snap-frozen in dry ice. All protocols were approved by the Salk Institute’s Institutional Animal Care and Use Committee (IACUC).
Libraries were constructed by Paired-seq workflow.

treatment_protocol: HepG2 and 3T3 cells were harvested by centrifugation, washed with PBS (Thermo Fisher Scientific) and counted using BioRad TC20 cell counter. The percentage of live cells should higher than 95%. The cells were then resuspended in cold Lysis Buffer (10 mM Tris-HCl pH 7.4 (Sigma), 10 mM NaCl (Sigma), 3 mM MgCl2 (Sigma), 0.1% IGEPAL CA-630 (Sigma)) and centrifuged for 15 min at 600 g, 4 °C. For the species mixing experiment, nuclei were then washed with PBS and resuspended, counted using BioRad TC20 cell counter. HepG2 and 3T3 nuclei were then mixed in equal proportions and applied to Paired-seq.

value: forebrain


title: WT1-1-MEGs; rep 1

status: Public on Nov 01 2019

type: SRA

city: Philadelphia

first: Jason

middle: Adam

last: Mills

state: PA

address: 422 Curie Blvd

department: Ophthalmology

country: USA

institute: The University of Pennsylvania

library_source: transcriptomic

data_processing:
Align pair-ended reads to reference genome using STAR (version 2.5.1b),  in a 2-pass mode.
The first pass mapped reads to known splice junctions in reference transcriptome (Illumina iGenome) during alignment while allowing for detection of novel junction sites.
Junction sites detected from multiple samples by the first pass were collected, combined and filtered.
The second pass re-aligned reads to the reference genome and transcriptome, plus the novel junction sites detected by the first pass.
Aligned reads were mapped to known genes. Only reads with both ends uniquely mapped to a gene were assigned to that gene to get its read count. Read counts of 3 technical replicates were combined.
Genome_build: NCBI GRCh38
Supplementary_files_format_and_content: Tab-delimited text file inclduing an integer matrix of gene-level read counts.

molecule: total RNA

organism: Homo sapiens

source_name: Megakaryocytes (MEGs)

growth_protocol: Megakaryocyte cells were generated as previosly published (Mills JA et al. 2013, Blood).  Megakarycoytes were generated in SFD + TPO + SCF + ascorbic acid media at 37C in 5% CO2 and expanded for 5 days before collection and analysis.

extract_protocol:
Samples were collected and total RNA was isolated using Trizol reagent then collected on Purelink RNA isolation column with DNASE treatment
RNA-seq libraries were prepared with Illumina TruSeq RiboZero Sample Prep kits.  Samples sequenced on a HiSeq 2500 (Illumina), using the paired end protocol with 125 bp read length to obtain three technical sequencing replicates per sample, each individual had three techincal replicates

tag: cell type

value: iPSC-derived megakaryocytes

tag: Stage

value: Day 12 post-induction

tag: genotype

value: CTRL


title: Nucleus Slc32a1-Cre:H2BG Vg_K18

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
SS2_16_033_Slc32a1_counts.txt
SS2_16_striatal_nuclei_counts.txt

data_processing:
fastq files were aligned to mouse genome version mm10
 The alignments of reads towards the indicated genome assembly using SAMtools
The expression values were computed per gene as described in Ramsköld et al (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo
Clustering and marker identification was done using the Seurat package in R (versions 1.4.0 and 2.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene

organism: Mus musculus

source_name: Slc32a1-Cre nucleus striatum

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: background strain

tag: treatment

value: untreated


title: Fetal Forebrain Lib#2 DNA

city: New York

library_source: genomic

molecule: genomic DNA

tag: tissue


title: Nucleus Slc32a1-Cre:H2BG Vg_K16


title: Nucleus Slc32a1-Cre:H2BG Vg_K17


title: CDLS3-3-HPCs; rep 3

source_name: Hematopoeitic progenitors (HPCs)

value: Human derived -HPC

value: Day 7 post-induction

value: NIPBL+/-


title: Nucleus Slc32a1-Cre:H2BG Vg_K15


title: Fetal Forebrain Lib#1 RNA


title: Nucleus Slc32a1-Cre:H2BG Vg_K13


title: CDLS3-2-HPCs; rep 2


title: Fetal Forebrain Lib#1 DNA


title: Nucleus Slc32a1-Cre:H2BG Vg_K12


title: Nucleus Slc32a1-Cre:H2BG Vg_K14


title: CDLS3-1-HPCs; rep 1


title: Nucleus Slc32a1-Cre:H2BG Vg_K11


title: Adult Cerebral Cortex Lib#3 RNA

source_name: Adult Brain

value: cerebral cortex


title: Nucleus Slc32a1-Cre:H2BG Vg_K10


title: Nucleus Slc32a1-Cre:H2BG Vg_K8


title: Adult Cerebral Cortex Lib#2 RNA


title: Nucleus Slc32a1-Cre:H2BG Vg_K7


title: CDLS2-2-HPCs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_K6


title: Adult Cerebral Cortex Lib#3 DNA


title: CDLS2-1-HPCs; rep 1


title: Adult Cerebral Cortex Lib#2 DNA


title: Nucleus Slc32a1-Cre:H2BG Vg_K4


title: Adult Cerebral Cortex Lib#1 RNA


title: CDLS1-3-HPCs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_K3


title: Nucleus Slc32a1-Cre:H2BG Vg_K5


title: Nucleus Slc32a1-Cre:H2BG Vg_K2


title: Adult Cerebral Cortex Lib#1 DNA


title: Nucleus Slc32a1-Cre:H2BG Vg_J24


title: Nucleus Slc32a1-Cre:H2BG Vg_K1


title: CDLS1-2-HPCs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_J22


title: Nucleus Slc32a1-Cre:H2BG Vg_J23


title: CDLS1-1-HPCs; rep 1


title: Nucleus Slc32a1-Cre:H2BG Vg_J21


title: CDLS2-3-HPCs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_J20


title: RNA170301TP_L361P_S19

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

data_processing:
FastQC was used for checking the quality of the raw sequence data.
Sequence data were then aligned using Spliced Transcripts Alignment to a Reference (STAR; Dobin et al., 2013), allowing for a maximum of 3 mismatches per 100 bp read. Reads were uniquely aligned greater than 88%, for all samples.
Reads were mapped to known genomic features to generate counts at the gene level using FeatureCounts (SubRead package).
Gene expression data were imported into R and an upper-quartile normalization was performed using edgeR (in R). Inclusion in the network analysis required a gene read density threshold of an average of greater than 1 count per million (CPM).
Network connectivity for coexpression and cosplicing were calculated
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: obtained with featureCounts from the package SubRead

source_name: Low Drinker_Pre-Frontal Cortex

growth_protocol: We used mass selection procedures to generate the third replicate set of the MA high and low drinking lines. The originating population for these lines was a B6D2F2 (F2) cross, and methods were precisely as described for the replicate 1 and 2 lines (Shabani et al, 2011[22]; Wheeler et al. 2009[10]). The founding population of 120 F2 mice (60 per sex; 53-56 days of age on the initial day of testing) was tested in a 2-bottle choice examination of water vs. MA intake. Briefly, mice were isolate housed and given access to 2, water-filled 25 ml graduated volumetric drinking tubes for 2 consecutive days. For the next 8 d, mice were offered a tube containing tap water and one containing MA dissolved in tap water. The concentration of MA was 20 mg/l for the first 4 d, and was increased to 40 mg/l for the next 4 days. The water tube remained on the cage for 24 h/d, while the MA-containing cylinder was available for 18 h/d. Volume consumed was determined by reading graduated markings on the tubes, and body weight was measured every 2 days and used with the volume data to calculate amount of MA consumed in mg/kg. MA intake when the 40 mg/l MA solution was available was used as the selection phenotype, and the highest consuming 26 F2 individual mice (half of each sex) were paired to establish the high line, whereas the lowest consuming 26 F2 mice were paired to establish the low line. Selection continued in this fashion across 5 generations (S1-S5), with S4 being that last offspring generation tested for MA intake. Within each line, 60 mice were tested each generation (30 per sex). Justifications for the overall procedures are detailed in our previous publications (Shabani et al, 2011[22]; Wheeler et al. 2009[10]).

extract_protocol:
Mice were euthanized by cervical dislocation and then immediately decapitated. The brain was removed using RNase free tools, rinsed in cold saline, and then the regions of interest were dissected out using RNase free tools and an aluminum dissection stage. The dissected regions were placed independently into RNase-free microcentrifuge tubes containing TRIzol (Life Science Technologies, Carlsbad, CA, USA) and immediately frozen on dry ice. Samples were stored at -80°C for no longer than 1 month prior to RNA extraction. The prefrontal cortex (PFC) was removed as the medial third of a 1.5-mm slice from the anterior part of the brain just behind the olfactory bulbs. The next 1.4-mm slice included the nucleus accumbens (NAc), which was taken using a micropunch fashioned from a 16-gauge blunt cut needle; the anterior commissure was used as a landmark. Next, using the superior colliculus as a landmark, the most anterior portion of the brain was removed and discarded, and the next 1-mm slice was taken, from which the ventral midbrain (VMB) was obtained. This included the remaining tissue after the ventral third of that slice and the cerebral cortex were removed. Total RNA was isolated from dissected tissue with TRIzol, using a modified single-step acid guanidinium thiocyanate-phenol-chloroform extraction method (Chomczynski and Sacchi, 1987[23]). The extracted RNA was purified using a RNAeasy kit (Qiagen, Velencia, VA USA), with RNA purity and concentration determined by NanoDrop spectrophotometry (ND-1000, Thermo Scientific, Wilmington, DE, USA). All samples submitted to the Massively Parallel Sequencing Shared Resource (MPSSR) for processing met criteria of 260/280 nm absorption ratio greater than 1.8 and greater than 100 ng of total RNA. Within the MPSSR, an RNA Integrity Number (RIN) was generated for each sample, using a Caliper LabChip GX, with an inclusion criterion of RIN > 9 for library formation. A total of 144 samples were included, 24 per line per brain region.
Library formation (polyA+, stranded) and sequencing were performed according to Illumina’s specifications at the MPSSR. Libraries were multiplexed, 4 per lane, yielding approximately 50 million total reads per sample

treatment_protocol: For the RNA-Seq analysis, we obtained brain tissue from experimentally naïve, non-MA exposed replicate 3 high and low line mice from second or later litters of generation S5. Animals were 60 - 86 days of age at the time of tissue harvesting (mean ± SEM = 69 ± 1 d). On the day of tissue harvesting, the group-housed male mice (2-3 per cage) were moved from the colony room, 4 h prior to tissue collection to allow them to acclimate to the procedure room environment. Sex has not impacted the response to selection for MA intake (Shabani et al., 2011[22]; Wheeler et al., 2009[10]), and male mice were used in our previous gene expression array studies (Shabani et al., 2011; Belknap et al., 2013[11]). Dissection occurred between 1100 and 1300 h.

tag: Sex

value: Male

tag: selected line

value: Low Drinker

value: Dissected Tissue (Brain) - Pre-Frontal Cortex


title: Nucleus Slc32a1-Cre:H2BG Vg_K9


title: RNA170301TP_L351P_S5


title: Nucleus Slc32a1-Cre:H2BG Vg_J19


title: RNA170301TP_L342P_S3


title: WT4-2-HPCs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_J17


title: WT3-3-HPCs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_J18


title: Nucleus Slc32a1-Cre:H2BG Vg_J15


title: Nucleus Slc32a1-Cre:H2BG Vg_J13


title: Nucleus Slc32a1-Cre:H2BG Vg_J14


title: WT3-2-HPCs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_J12


title: RNA170301TP_L321P_S20


title: WT3-1-HPCs; rep 1


title: WT4-3-HPCs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_J11


title: Nucleus Slc32a1-Cre:H2BG Vg_J10


title: WT2-3-HPCs; rep 3


title: Nucleus Slc32a1-Cre:H2BG Vg_J9


title: RNA170301TP_L311P_S26


title: RNA170301TP_L303P_S15


title: WT2-2-HPCs; rep 2


title: WT2-1-HPCs; rep 1


title: RNA170301TP_L301P_S1


title: WT4-1-HPCs; rep 1


title: Nucleus Slc32a1-Cre:H2BG Vg_J6


title: Nucleus Slc32a1-Cre:H2BG Vg_J16


title: Nucleus Slc32a1-Cre:H2BG Vg_J8


title: Nucleus Slc32a1-Cre:H2BG Vg_J4


title: RNA170301TP_L333P_S4


title: Nucleus Slc32a1-Cre:H2BG Vg_J5


title: Nucleus Slc32a1-Cre:H2BG Vg_J3


title: WT1-3-HPCs; rep 3


title: RNA170301TP_L292P_S12


title: RNA170301TP_L331P_S31


title: WT1-2-HPCs; rep 2


title: Nucleus Slc32a1-Cre:H2BG Vg_I23


title: WT1-1-HPCs; rep 1


title: Nucleus Slc32a1-Cre:H2BG Vg_J1


title: RNA170301TP_L273P_S13


title: cyaC-OE 4

type: RNA

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description:
GSM3356435
Replicate 4
Gene expression in cyaC-OE.

hyb_protocol: For each array, 19 µL of the purified Cy3-labeled cRNA (600 ng) was mixed with 5 µL of 10× Blocking Agent, 1 µL of 25× Fragmentation Buffer, and 25 µL of 2× GE Hybridization Buffer HI-RPM. The resultant mixtures were hybridized to the arrays at 65ºC for 17 h. After hybridization, each microarray slide was washed with Gene Expression wash buffer 1 at room temperature for 1 min, followed by Gene Expression wash buffer 2 at 37ºC for 1min.

scan_protocol: Slides were air dried for 1 min and scanned using an Agilent DNA Microarray Scanner at 5-µm resolution.

data_processing:
Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using the limma software package (version 3.36.2; https://www.bioconductor.org/packages/release/bioc/html/limma.html).
Processed_data.txt file includes log2-transformed normalized signal intensities.

organism: Shewanella oneidensis

source_name: cyaC-OE

label_protocol: Cyanine3 (Cy3)-labeled cRNA was synthesized from 25 ng of total RNA using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) and purified using a RNeasy Mini Kit (Qiagen). The labeled cRNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: An electrochemical cell was inoculated with MR-1(pBBR1MCS-2) or cyaC-OE cells at an initial optical density at 600 nm of 0.1, and was kept for 4 h at a working electrode potential of +0.4 V (vs. the standard hydrogen electrode).

extract_protocol: Total RNA was extracted using a Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and subsequently purified using an RNeasy Mini Kit and an RNase-Free DNase Set (Qiagen, Valencia, CA). The quality of total RNA was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Pico reagents and RNA Pico Chips (Agilent Technologies) according to the manufacturer’s instruction.

treatment_protocol: Bacterial cells attached to the working electrodes were collected.

tag: strain

value: cyaC-OE


title: Nucleus Slc32a1-Cre:H2BG Vg_I22


title: Nucleus Slc32a1-Cre:H2BG Vg_J7


title: RNA170301TP_L271P_S10


title: Nucleus Slc32a1-Cre:H2BG Vg_I21


title: Nucleus Slc32a1-Cre:H2BG Vg_I20


title: cyaC-OE 3

description:
GSM3356434
Replicate 3
Gene expression in cyaC-OE.


title: RNA170301TP_L293P_S6


title: Nucleus Slc32a1-Cre:H2BG Vg_I19


title: Nucleus Slc32a1-Cre:H2BG Vg_I18


title: Nucleus Slc32a1-Cre:H2BG Vg_I17


title: cyaC-OE 1

description:
GSM3356432
Replicate 1
Gene expression in cyaC-OE.


title: RNA170301TP_L261P_S21


title: RNA170301TP_L262P_S5


title: Nucleus Slc32a1-Cre:H2BG Vg_I16


title: Nucleus Slc32a1-Cre:H2BG Vg_I14


title: cyaC-OE 2

description:
GSM3356433
Replicate 2
Gene expression in cyaC-OE.


title: Nucleus Slc32a1-Cre:H2BG Vg_J2


title: Nucleus Slc32a1-Cre:H2BG Vg_I15


title: Nucleus Slc32a1-Cre:H2BG Vg_I12


title: RNA170301TP_L253P_S12


title: RNA170301TP_L251P_S2


title: RNA170301TP_L282P_S9


title: MR-1(pBBR1MCS-2) 4

description:
GSM3356431
Replicate 4
Gene expression in MR-1 (pBBR1MCS-2).

value: MR-1 (pBBR1MCS-2)


title: Nucleus Slc32a1-Cre:H2BG Vg_I24


title: Nucleus Slc32a1-Cre:H2BG Vg_I11


title: RNA170301TP_L221P_S28


title: Nucleus Slc32a1-Cre:H2BG Vg_I10


title: RNA170301TP_L213P_S6


title: Nucleus Slc32a1-Cre:H2BG Vg_I9


title: Nucleus Slc32a1-Cre:H2BG Vg_I7


title: Nucleus Slc32a1-Cre:H2BG Vg_I8


title: MR-1(pBBR1MCS-2) 1

description:
GSM3356428
Replicate 1
Gene expression in MR-1 (pBBR1MCS-2).


title: Nucleus Slc32a1-Cre:H2BG Vg_I6


title: Nucleus Slc32a1-Cre:H2BG Vg_I13


title: Nucleus Slc32a1-Cre:H2BG Vg_I5


title: RNA170301TP_L202P_S7


title: Nucleus Slc32a1-Cre:H2BG Vg_I3


title: MR-1(pBBR1MCS-2) 3

description:
GSM3356430
Replicate 3
Gene expression in MR-1 (pBBR1MCS-2).


title: Nucleus Slc32a1-Cre:H2BG Vg_I1


title: MR-1(pBBR1MCS-2) 2

description:
GSM3356429
Replicate 2
Gene expression in MR-1 (pBBR1MCS-2).


title: Nucleus Slc32a1-Cre:H2BG Vg_H24


title: RNA170301TP_H92P_S5

source_name: High Drinker_Pre-Frontal Cortex

value: High Drinker


title: RNA170301TP_L193P_S7


title: Nucleus Slc32a1-Cre:H2BG Vg_H22


title: RNA170301TP_L191P_S30


title: Nucleus Slc32a1-Cre:H2BG Vg_H20


title: Nucleus Slc32a1-Cre:H2BG Vg_H23


title: Nucleus Slc32a1-Cre:H2BG Vg_H21


title: RNA170301TP_L212P_S24


title: Nucleus Slc32a1-Cre:H2BG Vg_H19


title: Nucleus Slc32a1-Cre:H2BG Vg_H18


title: Nucleus Slc32a1-Cre:H2BG Vg_I4


title: Nucleus Slc32a1-Cre:H2BG Vg_H17


title: Nucleus Slc32a1-Cre:H2BG Vg_I2


title: Nucleus Slc32a1-Cre:H2BG Vg_H16


title: RNA170301TP_H71P_S18


title: RNA170301TP_H83P_S11


title: RNA170301TP_H61P_S3


title: Nucleus Slc32a1-Cre:H2BG Vg_H14


title: RNA170301TP_H91P_S1


title: RNA170301TP_H51P_S22


title: Nucleus Slc32a1-Cre:H2BG Vg_H11


title: Nucleus Slc32a1-Cre:H2BG Vg_H10


title: Nucleus Slc32a1-Cre:H2BG Vg_H12


title: Nucleus Slc32a1-Cre:H2BG Vg_H9


title: NRF2-/- LPS Placenta at E17, biological replicate 4

city: Baltimore

first: Thomas

middle: E

last: Sussan

state: MD

address: 615 N. Wolfe Street

department: Environmental Health & Engineering

institute: Johns Hopkins Bloomberg School of Public Health

description: Gene expression data from placenta of NRF2-/- animals administered intrauterine injections of LPS at day E17.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezg R package (version 17.0.0).

label: biotin

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Mouse placenta isolated at embryonic day 17

extract_protocol: Placentas were isolated and frozen in liquid nitrogen. RNA was isolated using RNEasy (Qiagen), and RNA integrity was determined by an Agilent 2100 Bioanalyzer

treatment_protocol: Intrauterine LPS or PBS

tag: genotype/strain

value: Intrauterine LPS

value: Placenta

tag: embryonic stage


title: Nucleus Slc32a1-Cre:H2BG Vg_H7


title: Nucleus Slc32a1-Cre:H2BG Vg_H15


title: Nucleus Slc32a1-Cre:H2BG Vg_H8


title: Nucleus Slc32a1-Cre:H2BG Vg_H6


title: Nucleus Slc32a1-Cre:H2BG Vg_H13


title: RNA170301TP_H22P_S17


title: RNA170301TP_H31P_S29


title: RNA170301TP_H41P_S11


title: RNA170301TP_H21P_S8


title: Nucleus Slc32a1-Cre:H2BG Vg_H2


title: Nucleus Slc32a1-Cre:H2BG Vg_H4


title: Nucleus Slc32a1-Cre:H2BG Vg_H3


title: RNA170301TP_H182P_S2


title: Nucleus Slc32a1-Cre:H2BG Vg_H5


title: Nucleus Slc32a1-Cre:H2BG Vg_H1


title: Nucleus Slc32a1-Cre:H2BG Vg_G24


title: RNA170301TP_H173P_S6


title: WT LPS Placenta at E17, biological replicate 4

description: Gene expression data from placenta of WT animals administered intrauterine injections of LPS at day E17.

source_name: WT Placenta


title: Nucleus Slc32a1-Cre:H2BG Vg_G22


title: NRF2-/- LPS Placenta at E17, biological replicate 2


title: NRF2-/- LPS Placenta at E17, biological replicate 3


title: Nucleus Slc32a1-Cre:H2BG Vg_G21


title: Nucleus Slc32a1-Cre:H2BG Vg_G20


title: Nucleus Slc32a1-Cre:H2BG Vg_G19


title: CF patient sample visit 4

city: Braunschweig

first: Diego

last: Chaves-Moreno

address: inhoffenstrasse 7

department: Department of Medical Microbiology (MMIK)

country: Germany

institute: Helmholtz Centrum for Infection Research

data_processing:
Cluster generation on HiSeq SR Flow Cell v3 generated at cBot using TruSeq SR Cluster Kit v3 – HS to create single- molecule DNA templates followed by bridge amplification. Sequencing run performed at HiSeq 2500 using TruSeq SBS Kit v3 (50 cycle) to run 51 cycles and 7 cycles for the single-indexed read.
Reference genome, and features files were obtained from S. aureus strain: CFBR-105, accession:GCA_003431365.1 wich were downloaded from the ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/431/365/GCF_003431365.1_ASM343136v1
Alignment was performed with Bowtie2 (Version: 2.3.4.1) on the very sensitive mode, Sam file was later converted in to Bam for further analysis  via samtools view
R processing of the alignments, 1. Features counts (Subread R package), were loaded from  the gff file and exons were obtained. 2. Sam files were loaded and expression was quantified by the use of the function summarizeOverlaps from the R package GenomicAlignments, ran on the union mode.
RPM values were calculated by the use of the function: returnRPKM form the package systempipeR  (V. 1.16.1 ) and  TPM values were calculated with an in-house function build in R
Supplementary_files_format_and_content: raw counts and TPM

organism: Staphylococcus aureus

source_name: Sputa

growth_protocol: Sputum amples were collected from CF patients at their visits

extract_protocol:
RNA was extracted using Qiagen's Rneasy Mini Kit following manufacturer's instructions, the where the samples were treated by beat beating in a solution of RLT Buffer (Qiagen) and 1% of β-mercaptoethanol.
ScriptSeq v2 RNA-Seq Library Preparation Kit for Low-input  (Epicentre) according to the manufacturer’s instructions using approximately 20 ng of input RNA
The libraries were size selected in a range of 200-500 bp using Blue Pippin

treatment_protocol: Sputolysin treatment for 30 minutes at 37 celsius degrees

tag: sample type

value: sputum


title: WT LPS Placenta at E17, biological replicate 1


title: CF patient sample visit 2


title: NRF2-/- Control Placenta at E17, biological replicate 3

description: Gene expression data from placenta of NRF2-/- animals administered intrauterine injections of PBS at day E17.

value: Intrauterine PBS


title: Nucleus Slc32a1-Cre:H2BG Vg_G17


title: WT LPS Placenta at E17, biological replicate 2


title: Nucleus Slc32a1-Cre:H2BG Vg_G18


title: WT LPS Placenta at E17, biological replicate 3


title: Nucleus Slc32a1-Cre:H2BG Vg_G16


title: RNA170301TP_H161P_S25


title: Nucleus Slc32a1-Cre:H2BG Vg_G15


title: RNA170301TP_H151P_S16


title: RNA170301TP_H152P_S27


title: RNA170301TP_H143P_S10


title: RNA170301TP_H141P_S7


title: Nucleus Slc32a1-Cre:H2BG Vg_G23


title: NRF2-/- Control Placenta at E17, biological replicate 1


title: NRF2-/- Control Placenta at E17, biological replicate 2


title: Nucleus Slc32a1-Cre:H2BG Vg_G14


title: RNA170301TP_H131P_S9


title: Nucleus Slc32a1-Cre:H2BG Vg_G13


title: Nucleus Slc32a1-Cre:H2BG Vg_G12


title: Nucleus Slc32a1-Cre:H2BG Vg_G11


title: Nucleus Slc32a1-Cre:H2BG Vg_G9


title: Nucleus Slc32a1-Cre:H2BG Vg_G10


title: RNA170301TP_H121P_S14


title: Nucleus Slc32a1-Cre:H2BG Vg_G8


title: RNA170301TP_H11P_S32


title: RNA170301TP_H101P_S4


title: RNA170301TP_H103P_S8


title: NRF2-/- LPS Placenta at E17, biological replicate 1


title: RNA170228TP_L371V_S11

source_name: Low Drinker_Ventral Midbrain

value: Dissected Tissue (Brain) - Ventral Midbrain


title: RNA170301TP_H112P_S8


title: RNA170301TP_H113P_S23


title: WT Control Placenta at E17, biological replicate 2

description: Gene expression data from placenta of WT animals administered intrauterine injections of PBS at day E17.


title: Nucleus Slc32a1-Cre:H2BG Vg_G5


title: Nucleus Slc32a1-Cre:H2BG Vg_F22


title: Nucleus Slc32a1-Cre:H2BG Vg_G6


title: Nucleus Slc32a1-Cre:H2BG Vg_G4


title: Nucleus Slc32a1-Cre:H2BG Vg_F19


title: Nucleus Slc32a1-Cre:H2BG Vg_G1


title: Nucleus Slc32a1-Cre:H2BG Vg_F23


title: Nucleus Slc32a1-Cre:H2BG Vg_F24


title: Nucleus Slc32a1-Cre:H2BG Vg_F18


title: Bone marrow stromal cells, S1213

city: Berlin

first: Karsten

last: Jürchott

address: Luisenstraße

department: Rahel Hirsch Center

institute: BIH at Charité

data_processing:
HiSeq Control Software 2.2.58,  Basecall: RTA 1.18.64.0
FastQ generation: bcl2fastq 1.8.4, FastQ trimming: Trimmomatic 0.36 (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:3:20 MINLEN:36), alignment: tophat 2.1.0 with bowtie2 2.2.5 and samtools 0.1.19 (--no-novel-juncs)
Reads were summarized per gene using the featureCount algorithm implemented in the R package Rsubread (v1.16.1).
Raw counts of protein-coding genes were normalized either using varianceStabilizingTransformation or normTransform function of the DESeq2 package (v1.6.3) (pseudocount=1, log2-transformation).
Genome_build: iGenome Homo_sapiens/Ensembl/GRCh38
Supplementary_files_format_and_content: Raw counts - tab-deliminated file with reads summerized per gene.
Supplementary_files_format_and_content: Variancestablized transformed data (vst) - tab-deliminated file with normalized and variance stabilizing transformed data of protein-coding genes
Supplementary_files_format_and_content: Normalized data (norm) - tab-deliminated file with normalized and log2-transformed data (pseudocount=1) of protein-coding genes

molecule: polyA RNA

source_name: bone marrow stromal cells

growth_protocol: The cells were isolated from metaphyseal bone marrow (BM) biopsies from patients undergoing hip replacement at Charité University Hospital. Briefly, the BM mononuclear cell fraction (BM-MNC) in primary BM and the BMSC fraction post Ficoll-density gradient centrifugation (Histopaque 1077; Sigma-Aldrich) were quantified with an automated electrical impedance-based CASYR Cell Counter (Schaerfe System GmbH). The BMSCcontaining interphase was plated in a 300 cm2 tissue culture flask (ThermoFischer) and cultured under standard conditions (37◦C, 5% CO2) in an expansion medium (Dulbecco’s Modified Eagle Medium-Low Glucose [DMEM-LG; Sigma-Aldrich] containing 10% fetal calf serum [FCS; Biochrom AG], 100 U/mL penicillin, and 100μg/mL streptomycin [Biochrom AG], and 2mM L-alanyl-L-glutamine [GlutaMAX; Gibco]). The non-adherent fraction was removed by washing with PBS (Gibco), the medium was changed every 72 h, and the cells were allowed to reach about 80% confluence before passaging. The BMSCs were then expanded for several passages and were characterized with multiple functional and molecular assays, in line with the minimal criteria of the International Society for Cellular Therapy (ISCT) (69), at passage three (P3, early  passage) and six (P6, late passage).

extract_protocol:
Total RNA was extracted by using the Qiagen RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions.
Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturers requirements. mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq system with High Output chemistry v4 (50 cycles, single-read)

treatment_protocol: A subset of n = 7 donors was treated for 24 h with or without cytokines (TNF-alpha and IFN-gamma, both 10 ng/mL), which werematched to the corresponding unstimulated cells and processed in parallel.

tag: donor

tag: gender

value: F

tag: age

tag: diabetes

value: h

tag: passage

tag: stimulation

value: REST

value: bone marrow-derived stromal cells (BMSC)


title: Nucleus Slc32a1-Cre:H2BG Vg_G3

value: untreated


title: Nucleus Slc32a1-Cre:H2BG Vg_G7


title: Nucleus Slc32a1-Cre:H2BG Vg_F20


title: Nucleus Slc32a1-Cre:H2BG Vg_G2


title: Nucleus Slc32a1-Cre:H2BG Vg_F21


title: WT Control Placenta at E17, biological replicate 1


title: RNA170228TP_L361V_S1


title: Bone marrow stromal cells, S1210

value: d (IDDM)

tag: cell type


title: Nucleus Slc32a1-Cre:H2BG Vg_F17

tag: genotype


title: Bone marrow stromal cells, S1216

value: STIM


title: Nucleus Slc32a1-Cre:H2BG Vg_F16

tag: background strain


title: Nucleus Slc32a1-Cre:H2BG Vg_F12

tag: treatment


title: Bone marrow stromal cells, S1212

value: M


title: Nucleus Slc32a1-Cre:H2BG Vg_F15


title: Nucleus Slc32a1-Cre:H2BG Vg_F13


title: Bone marrow stromal cells, S1214


title: RNA170228TP_L351V_S15

value: Male

value: Low Drinker

tag: tissue


title: RNA170228TP_L321V_S1

tag: Sex


title: Nucleus Slc32a1-Cre:H2BG Vg_F11


title: Bone marrow stromal cells, S1211


title: RNA170228TP_L342V_S6

tag: selected line


title: Bone marrow stromal cells, S1215


title: Bone marrow stromal cells, S1209


title: NRF2-/- Control Placenta at E17, biological replicate 4


title: Bone marrow stromal cells, S1207


title: RNA170228TP_L333V_S13


title: Nucleus Slc32a1-Cre:H2BG Vg_F14


title: WT Control Placenta at E17, biological replicate 3


title: RNA170228TP_L303V_S21


title: RNA170228TP_L311V_S25


title: RNA170228TP_L301V_S19


title: Nucleus Slc32a1-Cre:H2BG Vg_F9


title: Nucleus Slc32a1-Cre:H2BG Vg_F8


title: Nucleus Slc32a1-Cre:H2BG Vg_F6


title: Nucleus Slc32a1-Cre:H2BG Vg_F5


title: Bone marrow stromal cells, S1208


title: Nucleus Slc32a1-Cre:H2BG Vg_F4


title: Nucleus Slc32a1-Cre:H2BG Vg_F3


title: RNA170228TP_L292V_S12


title: Nucleus Slc32a1-Cre:H2BG Vg_F2


title: Nucleus Slc32a1-Cre:H2BG Vg_F1


title: Nucleus Slc32a1-Cre:H2BG Vg_E23


title: Nucleus Slc32a1-Cre:H2BG Vg_E24


title: miR-K6-5p 5'U replicate 2

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

data_processing:
Sequencing reads were aligned to STAR. Read counts were generated with HTSeq and differential gene expression analyses were performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts (HTSeq)

source_name: miR-K6-5p 5'U

growth_protocol: HEK 293T NoDice cells were maintained in Dulbecco modified Eagle medium (DMEM) containing 4.5 g/liter glucose and L-glutamine (Corning), supplemented with 10% Serum Plus-II (Sigma-Aldrich) and gentamicin.

extract_protocol:
Media was removed from cells. Cells were then lysed in Trizol reagent. RNA was isolated using Direct-zol RNA MiniPrep Plus (Zymo Research), skipping the optional DNase treatment step, eluting in 100uL water.
Sequencing libraries were constructed using Illumina TruSeq RNA  Library Prep Kit with oligo-dT beads.

treatment_protocol: HEK 293T NoDice cells were seeded at the density 83,333 cells/cm2 in 6-well plates (Falcon). One day post seeding, cells were transfected with 10nM control, miR-16, miR-214, miR-K6-5p  wild-type, or miR-K6 5’U mimic (miRVana) with lipofectamine RNAiMAX as described by manufacturer. Two days post-transfection, cells were harvested to extract RNA.

tag: cell line

value: HEK293T NoDice

tag: transfection

value: miR-K6-5p 5'U mimic


title: miR-K6-5p 5'U replicate 3


title: Nucleus Slc32a1-Cre:H2BG Vg_E22


title: miR-K6-5p 5'U replicate 1


title: Nucleus Slc32a1-Cre:H2BG Vg_E21


title: Nucleus Slc32a1-Cre:H2BG Vg_F7


title: Nucleus Slc32a1-Cre:H2BG Vg_F10


title: RNA170228TP_L273V_S23


title: RNA170228TP_L271V_S4


title: Nucleus Slc32a1-Cre:H2BG Vg_E19


title: miR-K6-5p WT replicate 3

source_name: miR-K6-5p WT

value: miR-K6-5p WT mimic


title: Nucleus Slc32a1-Cre:H2BG Vg_E20


title: WT Control Placenta at E17, biological replicate 4

tag: genotype/strain

value: Placenta

tag: embryonic stage


title: miR-K6-5p WT replicate 2


title: Nucleus Slc32a1-Cre:H2BG Vg_E16


title: RNA170228TP_L282V_S5


title: Nucleus Slc32a1-Cre:H2BG Vg_E17


title: Nucleus Slc32a1-Cre:H2BG Vg_E15


title: miR-214 replicate 3

value: miR-214 mimic


title: miR-K6-5p WT replicate 1


title: RNA170228TP_L253V_S20


title: RNA170228TP_L261V_S30


title: RNA170228TP_L262V_S28


title: miR-214 replicate 2


title: Nucleus Slc32a1-Cre:H2BG Vg_E14


title: miR-214 replicate 1


title: miR-16 replicate 3

value: miR-16 mimic


title: RNA170228TP_L231V_S2

value: Dissected Tissue (Brain) - Ventral Midbrain


title: RNA170228TP_L251V_S3


title: RNA170228TP_L221V_S6


title: RNA170228TP_L213V_S11


title: Nucleus Slc32a1-Cre:H2BG Vg_E7


title: Nucleus Slc32a1-Cre:H2BG Vg_E9


title: Nucleus Slc32a1-Cre:H2BG Vg_E8


title: Nucleus Slc32a1-Cre:H2BG Vg_E11


title: miR-16 replicate 2


title: Nucleus Slc32a1-Cre:H2BG Vg_E6


title: RNA170228TP_L212V_S8


title: Nucleus Slc32a1-Cre:H2BG Vg_E12


title: Nucleus Slc32a1-Cre:H2BG Vg_E5


title: Nucleus Slc32a1-Cre:H2BG Vg_E4


title: miR-16 replicate 1


title: Nucleus Slc32a1-Cre:H2BG Vg_E3


title: Nucleus Slc32a1-Cre:H2BG Vg_E1


title: Nucleus Slc32a1-Cre:H2BG Vg_E2


title: RNA170228TP_L193V_S32


title: Nucleus Slc32a1-Cre:H2BG Vg_D24


title: RNA170228TP_L202V_S10


title: RNA170228TP_L191V_S2


title: Control mimic replicate 2

source_name: Control mimic

value: Control mimic


title: RNA170228TP_H92V_S29

source_name: High Drinker_Ventral Midbrain

value: High Drinker


title: Nucleus Slc32a1-Cre:H2BG Vg_D23


title: Control mimic replicate 3


title: Nucleus Slc32a1-Cre:H2BG Vg_E10


title: Nucleus Slc32a1-Cre:H2BG Vg_E13


title: Nucleus Slc32a1-Cre:H2BG Vg_D22


title: Control mimic replicate 1


title: Nucleus Slc32a1-Cre:H2BG Vg_D21


title: RNA170228TP_H91V_S2


title: Nucleus Slc32a1-Cre:H2BG Vg_D18


title: Nucleus Slc32a1-Cre:H2BG Vg_D17


title: RNA170228TP_H83V_S7


title: Nucleus Slc32a1-Cre:H2BG Vg_D20


title: RNA170228TP_H81V_S27


title: Zc3h10 ChIP seq

city: Berkeley

first: Danielle

last: Yi

state: CA

address: 220 Morgan Hall

institute: UC Berkeley

data_processing:
Adapters were removed using FASTQ Groomer v1.1.1
Reads were aligned to reference genome mm10 using Map with BWA
Peaks were called using MACS
bigwig files were generated using Wig/Bedgraph-to-bigwig
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file is included for visualization of peaks using genome browser.

source_name: brown adipose tissue

growth_protocol: Mice were maintained on chow diet until 12 weeks of age.

extract_protocol:
Brown adipose tissue was crosslinked and minced, nuclei were isolated and sonicated.  Lysates were clarified and ChIP reactions were set up using Zc3h10 antibody.
Library construction and sequencing were performed by the UC Berkeley Functional Genomics laboratory (FGL) and the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley

treatment_protocol: Mice were sacrified at 12 weeks of age

value: brown adipose tissue

tag: strain

tag: chip antibody


title: Nucleus Slc32a1-Cre:H2BG Vg_D15


title: Nucleus Slc32a1-Cre:H2BG Vg_D16


title: Input DNA


title: Nucleus Slc32a1-Cre:H2BG Vg_D19


title: RNA170228TP_H71V_S22


title: SS2_6

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

data_processing:
10x: demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.0.
SS2: all reads aligned using STAR, count matrix generated using rpkmforgenes with options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, using file with unique positions from MULTo. Gene annotations used were transcripts in RefSeq.
Genome_build: mm10 (Ensembl 84)
Supplementary_files_format_and_content: 10x_fastq: fastq files of individual 10x samples; 10x_count: 10x count matrix in sparse matrix format; 10x_barcode: barcode ids per 10x sample; 10x_gene: gene ids per 10x sample; SS2_fastq: fastq.tar of all SS2 wells; SS2_count: SS2 count matrix in tabular format; SS2_ercc_count: SS2 ercc matrix in tabular format; SS2_layout: SS2 cell layout in csv format.

source_name: 3x Healthy_1x PF, 2x HSC_liver tissue

extract_protocol:
Enzymatic digestion and FACS
Smart-seq2

tag: disease status

value: 3x Healthy

tag: isolation protocol

value: 1x PF, 2x HSC

value: Liver (n=3 mice)


title: Nucleus Slc32a1-Cre:H2BG Vg_D14

value: untreated


title: SS2_5

source_name: 2x CCl4 6wk, 1x Healthy_3x PF_liver tissue

value: 2x CCl4 6wk, 1x Healthy

value: 3x PF


title: Nucleus Slc32a1-Cre:H2BG Vg_D12

source_name: Slc32a1-Cre nucleus striatum


title: Nucleus Slc32a1-Cre:H2BG Vg_D13


title: RNA170228TP_H61V_S1

value: Male


title: SS2_4

source_name: 1x BDL 14d, 1x Healthy_2x PF_liver tissue

value: 1x BDL 14d, 1x Healthy

value: 2x PF

value: Liver (n=2 mice)


title: SS2_3

source_name: 1x Healthy, 2x CCl4 6wk_3x PF_liver tissue

value: 1x Healthy, 2x CCl4 6wk


title: Nucleus Slc32a1-Cre:H2BG Vg_D11


title: Nucleus Slc32a1-Cre:H2BG Vg_D10


title: SS2_2

source_name: 2x BDL 14d, 1x Healthy_3x PF_liver tissue

value: 2x BDL 14d, 1x Healthy


title: Nucleus Slc32a1-Cre:H2BG Vg_D7


title: RNA170228TP_H41V_S10


title: Nucleus Slc32a1-Cre:H2BG Vg_D6


title: Nucleus Slc32a1-Cre:H2BG Vg_D8


title: RNA170228TP_H31V_S26


title: Nucleus Slc32a1-Cre:H2BG Vg_D4


title: RNA170228TP_H21V_S16


title: Nucleus Slc32a1-Cre:H2BG Vg_D3


title: Nucleus Slc32a1-Cre:H2BG Vg_D5


title: SS2_1


title: 10x_5

source_name: CCl4 6wk_PF_liver tissue

extract_protocol:
Enzymatic digestion and FACS
10x Genomics Single Cell 3' v2

value: CCl4 6wk

value: PF


title: 10x_4

source_name: Healthy_PF_liver tissue

value: Healthy


title: RNA170228TP_H51V_S18

value: High Drinker

value: Dissected Tissue (Brain) - Ventral Midbrain


title: Nucleus Slc32a1-Cre:H2BG Vg_D1


title: Nucleus Slc32a1-Cre:H2BG Vg_C24


title: Nucleus Slc32a1-Cre:H2BG Vg_D2


title: Nucleus Slc32a1-Cre:H2BG Vg_D9


title: Nucleus Slc32a1-Cre:H2BG Vg_C23


title: 10x_2

source_name: CCl4 72h_HSC_liver tissue

value: CCl4 72h

value: HSC


title: Nucleus Slc32a1-Cre:H2BG Vg_C21


title: Nucleus Slc32a1-Cre:H2BG Vg_C22


title: RNA170228TP_H171V_S8


title: RNA170228TP_H152V_S9


title: RNA170228TP_H182V_S9


title: RNA170228TP_H161V_S24


title: Nucleus Slc32a1-Cre:H2BG Vg_C18


title: RNA170228TP_H173V_S3


title: PLAC-seq E16.5 rep2

data_processing:
Library strategy: PLAC-seq
We performed PLAC-seq experiments on mouse E12.5 and E16.5 forebrain tissues, and applied our recently developed MAPS for the downstream data analysis. Specifically, we first used “bwa mem” to map the two ends of one paired-end reads to the reference genome mm10 separately, and then kept the valid mapped reads, and removed PCR duplicates by “samtools rmdup”. Next, we divided intra-chromosomal reads into short-range reads (<= 1 kb) and long-range reads (> 1 kb), and used the short-range reads to measure ChIP-enrichment level, and the long-range reads to measure chromatin interactions. We further binned the autosomal chromosomes (chr1-chr19) into consecutive, non-overlapping 10-kb bins, and selected 10-kb bin pairs where at least one bin contains H3K4me3 ChIP-seq peaks (since PLAC-seq is designed to measure protein-mediated chromatin interactions) for the downstream analysis. We have shown that PLAC-seq data contain multiple layers of systematic biases, including restriction enzyme cutting frequency, GC content, sequence mappability and ChIP-enrichment level. To normalize PLAC-seq data, we fitted a positive Poisson regression model for the selected 10-kb bin pairs, taking the raw contact frequency as the outcome and the aforementioned systematic biases and 1D genomic distance as predictors. We obtained expected contact frequency and P-value from the fitted positive Poisson regression model, and then converted P-value into false discovery rate (FDR). We defined a 10-kb bin pair as candidate significant interaction if the normalized contact frequency (the ratio between observed contact frequency and the expected contact frequency) is >=2, and the FDR < 1%. We further grouped candidate significant interactions together if they are within 10 kb. If a candidate significant interaction has no other significant interaction in neighborhood region, we defined it as a singleton, otherwise, we defined it as a peak cluster. Since biologically relevant interactions tend to cluster together and singletons are more likely to be false positives, we applied a more stringent FDR threshold 1e-4 for singletons. The final list of significant interactions consists of peak clusters with FDR < 1% and singletons with FDR < 1e-4.

source_name: Fetal Forebrain

extract_protocol: The nuclei were harvested at 2,500 g for 5 min and the supernatant was discarded. The nuclei were then resuspended in 130 μl RIPA buffer (10 mM Tris, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, proteinase inhibitors) and lysed on ice for 10 min, followed by sonication using Covaris M220. The samples were centrifugation at 14,000 rpm for 20 min and supernatant was collected. The clear cell lysate was incubated with H3K4me3 antibody-coated (04-745, Millipore, 5 μg per sample) Dynabead M-280 Sheep Anti-Rabbit IgG at 4°C overnight. After incubation, the beads were washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. To elute DNA, washed beads were first treated with 10 μg RNase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 h at 37 °C, followed by adding 20 μg proteinase K and incubate at 65 °C 2 h. The fragmented DNA was purified by Zymo DNA Clean&Concentrator kit. Biotinylated DNA was pulled-down by Dynabeads MyOne Streptavidin T1 beads and PCR amplified for sequencing.

treatment_protocol: The frozen tissues were pulverized prior to formaldehyde crosslinking. About 30-50 mg of frozen tissue were crosslinked with 1% formaldehyde at room temperature for 20 min. Dissociation of crosslinked tissues were performed with gentle MACS dissociator. Single-nuclei suspensions prepared from crosslinked tissues were incubated in 50 μl 0.5% of SDS and incubated at 62 °C for 10 min. 25 μl 10% Triton X-100 and 145 μl water were then added, followed by incubation at 37 °C for 15 min. Digestion was performed by MboI for 2 h 37 °C, followed by inactivation at 62 °C for 20 min. 15 nmol of dCTP, dGTP, dTTP, biotin-14-dATP (Thermo Fisher Scientific) each and 40 unit of Klenow were then added, and incubated at 37°C for 1.5h. Proximity ligation was performed at room temperature in 1X T4 DNA Ligase Buffer, 0.1 mg/ml BSA, 1% Triton X-100 and 4000 unit of T4 DNA Ligase (NEB).

value: forebrain

tag: developmental stage


title: PLAC-seq E16.5 rep1


title: Nucleus Slc32a1-Cre:H2BG Vg_C15

value: untreated


title: Nucleus Slc32a1-Cre:H2BG Vg_C14


title: RNA170228TP_H151V_S14


title: RNA170228TP_H141V_S31


title: PLAC-seq E12.5 rep2


title: 10x_3

source_name: CCl4 6wk_HSC_liver tissue

value: Liver (n=3 mice)


title: Nucleus Slc32a1-Cre:H2BG Vg_C12


title: RNA170228TP_H143V_S4


title: PLAC-seq E12.5 rep1

description: The nuclei were harvested at 2,500 g for 5 min and the supernatant was discarded. The nuclei were then resuspended in 130 μl RIPA buffer (10 mM Tris, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, proteinase inhibitors) and lysed on ice for 10 min, followed by sonication using Covaris M220. The samples were centrifugation at 14,000 rpm for 20 min and supernatant was collected. The clear cell lysate was incubated with H3K4me3 antibody-coated (04-745, Millipore, 5 μg per sample) Dynabead M-280 Sheep Anti-Rabbit IgG at 4°C overnight. After incubation, the beads were washed with RIPA buffer three times, high-salt RIPA buffer (10 mM Tris, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) twice, LiCl buffer (10 mM Tris, pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% IGEPAL CA-630, 0.1% sodium deoxycholate) once, TE buffer (10 mM Tris, pH 8.0, 0.1 mM EDTA) twice. To elute DNA, washed beads were first treated with 10 μg RNase A in extraction buffer (10 mM Tris, pH 8.0, 350 mM NaCl, 0.1 mM EDTA, 1% SDS) for 1 h at 37 °C, followed by adding 20 μg proteinase K and incubate at 65 °C 2 h. The fragmented DNA was purified by Zymo DNA Clean&Concentrator kit. Biotinylated DNA was pulled-down by Dynabeads MyOne Streptavidin T1 beads and PCR amplified for sequencing.

data_processing:
Library strategy: PLAC-seq
We performed PLAC-seq experiments on mouse E12.5 and E16.5 forebrain tissues, and applied our recently developed MAPS for the downstream data analysis. Specifically, we first used “bwa mem” to map the two ends of one paired-end reads to the reference genome mm10 separately, and then kept the valid mapped reads, and removed PCR duplicates by “samtools rmdup”. Next, we divided intra-chromosomal reads into short-range reads (<= 1 kb) and long-range reads (> 1 kb), and used the short-range reads to measure ChIP-enrichment level, and the long-range reads to measure chromatin interactions. We further binned the autosomal chromosomes (chr1-chr19) into consecutive, non-overlapping 10-kb bins, and selected 10-kb bin pairs where at least one bin contains H3K4me3 ChIP-seq peaks (since PLAC-seq is designed to measure protein-mediated chromatin interactions) for the downstream analysis. We have shown that PLAC-seq data contain multiple layers of systematic biases, including restriction enzyme cutting frequency, GC content, sequence mappability and ChIP-enrichment level68. To normalize PLAC-seq data, we fitted a positive Poisson regression model for the selected 10-kb bin pairs, taking the raw contact frequency as the outcome and the aforementioned systematic biases and 1D genomic distance as predictors. We obtained expected contact frequency and P-value from the fitted positive Poisson regression model, and then converted P-value into false discovery rate (FDR). We defined a 10-kb bin pair as candidate significant interaction if the normalized contact frequency (the ratio between observed contact frequency and the expected contact frequency) is >=2, and the FDR < 1%. We further grouped candidate significant interactions together if they are within 10 kb. If a candidate significant interaction has no other significant interaction in neighborhood region, we defined it as a singleton, otherwise, we defined it as a peak cluster. Since biologically relevant interactions tend to cluster together and singletons are more likely to be false positives, we applied a more stringent FDR threshold 1e-4 for singletons. The final list of significant interactions consists of peak clusters with FDR < 1% and singletons with FDR < 1e-4.

extract_protocol:
Male C57BL/6J mice were purchased from Jackson laboratories at 8 weeks of age and maintained in the Salk animal barrier facility on 12 hr dark-light cycles with food ad libitum for four weeks before dissection. Cerebral cortex was dissected and snap-frozen in dry ice. All protocols were approved by the Salk Institute’s Institutional Animal Care and Use Committee (IACUC).
Libraries were constructed by REACH-seq workflow.


title: Nucleus Slc32a1-Cre:H2BG Vg_C11


title: Nucleus Slc32a1-Cre:H2BG Vg_C10


title: Nucleus Slc32a1-Cre:H2BG Vg_C20


title: 10x_1

source_name: Healthy_HSC_liver tissue


title: Nucleus Slc32a1-Cre:H2BG Vg_C17


title: D6 differentiated

city: Neuherberg

first: Dominik

last: Lutter

address: Ingolstädter Landstraße 1

department: Institute for Diabetes and Obesity

institute: Helmholtz Zentrum München

data_processing:
STAR aligner was used for split-read alignment against the mouse genome assembly mm9 and UCSC known Gene annotation. To quantify the number of reads mapping to annotated genes, we used HTseq-count.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *.htseqcounts.tsv: Tab-delimited text files contain raw read counts; they have two columns, where the first column specifies the gene name and the second the actual read count.

growth_protocol: Murine brown pre-adipocytes were maintained in medium containing glucose, pyruvate, FBS and Pen-Strep. Cells were split and replated every 2 days.

extract_protocol:
RNA was extracted with RNeasy kit (Qiagen) following manufacturer's instruction.
For library preparation, 1 µg of total RNA per sample was used. RNA molecules were poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (EPF, Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the TruSeq Stranded mRNA Sample Preparation Guide (Illumina). RNA libraries were assessed for quality and quantity with the Agilent 2100 BioAnalyzer and the Quant-iT PicoGreen dsDNA Assay Kit (Life Technologies).
Strand-specific RNA libraries were sequenced as 100 bp paired-end runs on an Illumina HiSeq4000 platform.

treatment_protocol: IBMX, dexamethasone, indomethacin, T3 and insulin were added to induce differentiation. Cells were differentiated for 8 days, by subsequently changing medium (with T3 and insulin) every 2 days.

tag: strain/background

value: immortalised brown adipose cells

value: differentiated

tag: passage number


title: Nucleus Slc32a1-Cre:H2BG Vg_C19

tag: genotype


title: RNA170228TP_H121V_S5

value: Male


title: Nucleus Slc32a1-Cre:H2BG Vg_C8

tag: background strain


title: Nucleus Slc32a1-Cre:H2BG Vg_C7

tag: treatment


title: Nucleus Slc32a1-Cre:H2BG Vg_C16


title: Nucleus Slc32a1-Cre:H2BG Vg_C6


title: D5 differentiated

tag: cell type


title: Nucleus Slc32a1-Cre:H2BG Vg_C9


title: RNA170228TP_H11V_S7

tag: Sex

tag: tissue


title: Nucleus Slc32a1-Cre:H2BG Vg_C13


title: RNA170228TP_H113V_S12

tag: selected line


title: Nucleus Slc32a1-Cre:H2BG Vg_C5


title: D4 differentiated

tag: cell line


title: Nucleus Slc32a1-Cre:H2BG Vg_C4


title: RNA170228TP_H131V_S4


title: Nucleus Slc32a1-Cre:H2BG Vg_C3


title: RNA170228TP_H112V_S17


title: Nucleus Slc32a1-Cre:H2BG Vg_C2


title: Nucleus Slc32a1-Cre:H2BG Vg_C1


title: D2 differentiated


title: RNA170228TP_H101V_S3


title: D1 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B24


title: Nucleus Slc32a1-Cre:H2BG Vg_B22


title: RNA160225TP_9_H61NA

source_name: High Drinker_Nucleus Accumbens

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: Nucleus Slc32a1-Cre:H2BG Vg_B23


title: Nucleus Slc32a1-Cre:H2BG Vg_B21


title: RNA160225TP_8_H52NA


title: C6 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B19


title: D3 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B18


title: Nucleus Slc32a1-Cre:H2BG Vg_B7


title: RNA160225TP_6_H42NA


title: Nucleus Slc32a1-Cre:H2BG Vg_B16


title: RNA160225TP_7_H51NA


title: C3 differentiated


title: C2 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B14


title: Nucleus Slc32a1-Cre:H2BG Vg_B11


title: Nucleus Slc32a1-Cre:H2BG Vg_E18


title: RNA160225TP_44_L332NA

source_name: Low Drinker_Nucleus Accumbens

value: Low Drinker


title: C5 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B5


title: Nucleus Slc32a1-Cre:H2BG Vg_B4


title: Nucleus Slc32a1-Cre:H2BG Vg_B3


title: Nucleus Slc32a1-Cre:H2BG Vg_B2


title: RNA160225TP_43_L331NA


title: A6 differentiated


title: RNA160225TP_45_L342NA


title: RNA160225TP_42_L321NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A24


title: A5 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_A23


title: A3 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_A22


title: Nucleus Slc32a1-Cre:H2BG Vg_A21


title: Nucleus Slc32a1-Cre:H2BG Vg_B12


title: A2 differentiated


title: RNA160225TP_46_L343NA


title: C4 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B10


title: Nucleus Slc32a1-Cre:H2BG Vg_B13


title: Nucleus Slc32a1-Cre:H2BG Vg_A20


title: Nucleus Slc32a1-Cre:H2BG Vg_B17


title: RNA160225TP_40_L302NA


title: B5 differentiated


title: B6 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_B15


title: RNA160225TP_48_L372NA


title: Nucleus Slc32a1-Cre:H2BG Vg_B8


title: RNA160225TP_4_H31NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A19


title: Nucleus Slc32a1-Cre:H2BG Vg_B20


title: Nucleus Slc32a1-Cre:H2BG Vg_B9


title: RNA160225TP_41_L311NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A18


title: B4 differentiated


title: RNA160225TP_39_L293NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A17


title: Nucleus Slc32a1-Cre:H2BG Vg_A16


title: RNA160225TP_5_H41NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A13


title: Nucleus Slc32a1-Cre:H2BG Vg_A15


title: RNA160225TP_37_L273NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A12


title: Nucleus Slc32a1-Cre:H2BG Vg_A14


title: Nucleus Slc32a1-Cre:H2BG Vg_B6


title: Activated B cells_ Mouse 2

city: NORTH CHICAGO

first: Rahul

last: Vijay

address: 3333 GreenBay Road, BSB 2.450

department: Microbiology and Immunology

institute: Rosalind Franklin University

description: Sample name: 10

data_processing:
The quality of sequence reads was assessed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and were aligned using STAR aligner82 to the mouse genome version mm10
Differentially expressed genes were identified using Partek GS software and genes with significant changes were filtered using adjusted p- value of 0.05 as threshold
Ingenuity Pathway Analysis software (Qiagen Bioinformatics) was used to identify the underlying molecular pathways and interaction networks that involved the differentially expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized counts

source_name: Spleen

extract_protocol:
Spleen were harvested, single cell suspension made, ACK lysed and stained for B220, CD19, CD138 and IgD. Cells were sorted on FACS Aria and FACS Fusion cell sorters. RNA extracted using NucleoSpin RNA kit (Takara Bio USA Inc).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were infected with 1 million Py parasitzed RBCs i.v

tag: mouse strain

tag: infection

value: Plasmodium yoelli (Py)

tag: time

value: 10 days post infection

value: Spleen

value: Activated B cells

tag: surface markers


title: B3 differentiated


title: Nucleus Slc32a1-Cre:H2BG Vg_A11


title: Activated B cells_ Mouse 4

description: Sample name: 12


title: RNA160225TP_35_L263NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A10


title: RNA160225TP_36_L272NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A8


title: Resting B cells_Mouse 4

description: Sample name: 8

value: Resting B cells


title: Nucleus Slc32a1-Cre:H2BG Vg_A7


title: Activated B cells_ Mouse 1

description: Sample name: 9


title: Resting B cells_Mouse 3

description: Sample name: 7


title: RNA160225TP_34_L261NA


title: Nucleus Slc32a1-Cre:H2BG Vg_A6


title: Nucleus Slc32a1-Cre:H2BG Vg_A5


title: RNA160225TP_33_L253NA


title: Activated B cells_ Mouse 3

description: Sample name: 11


title: Nucleus Slc32a1-Cre:H2BG Vg_A4


title: Nucleus Slc32a1-Cre:H2BG Vg_A9


title: B1 differentiated


title: Resting B cells_Mouse 2

description: Sample name: 6


title: RNA160225TP_32_L251NA


title: Resting B cells_Mouse 1

description: Sample name: 5


title: Nucleus Slc32a1-Cre:H2BG Vg_A2


title: Nucleus Slc32a1-Cre:H2BG Vg_A1


title: RNA160225TP_30_L221NA


title: Plasmsablasts_Mouse3

description: Sample name: 3

value: Plasmsablasts


title: Plasmsablasts_Mouse4

description: Sample name: 4


title: Plasmsablasts_Mouse1

description: Sample name: 1


title: NS_WGBS_iCM_Day7_rep2

city: San Francisco

first: Nicole

last: Stone

address: 1650 Owens St.

institute: Gladstone Institutes - UCSF

description:
BC8
all.bsseq.matrix.txt.minustwocols.gz
all.dmr.Day7.txt
all.dmr.Day7.annotated.txt

data_processing:
Reads were trimmed using Fastq-mcf (http://code.google.com/p/ea-utils) and aligned to the mm9 genomic assembly.
Sequencing quality was assessed with FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and duplicate reads were removed using Picard MarkDuplicates (http://broadinstitute.github.io/picard).
Reads were aligned with Bismark (https://www.bioinformatics.babraham.ac.uk/projects/bismark/), and methylation calls were made with bismark_methylation_extractor using options: -p -no_overlap.
DMRs were identified using Bsseq (Hansen et al. 2012). We required minimum CpG content of >=3 and >=0.1 absolute difference in methylation for all DMRs.
Genome_build: mm9
Supplementary_files_format_and_content: Processed data files include Bsseq output matrix containing position specific methylation levels, text files containing dynamically methylated regions (DMR) resulting from comparisons of fibroblasts to day 3 and day 7 iCMs, and text files containing nearest gene information associated with all DMRs identified.
all.bsseq.matrix.txt.minustwocols.gz:  Bsseq output matrix in .gz compressed format, containing position specific methylation information.
all.colnames.minustwocols.txt:  Text file containing column headings for "all.bsseq.matrix.txt.minustwocols.gz".
all.dmr.Day3.annotated.txt:  Text file containing DMR locations resulting from comparison of Day 3 iCM vs Fibroblast, with nearest gene annotations.
all.dmr.Day3.txt:  Text file containing Bsseq output DMR information resulting from comparison of Day 3 iCM vs Fibroblast.
all.dmr.Day7.annotated.txt:  Text file containing DMR locations resulting from comparison of Day 7 iCM vs Fibroblast, with nearest gene annotations.
all.dmr.Day7.txt:  Text file containing Bsseq output DMR information resulting from comparison of Day 7 iCM vs Fibroblast.

source_name: neonatal mouse heart

extract_protocol:
Genomic DNA was isolated using the Qiagen DNeasy Blood and Tissue kit (Cat No./ID: 69504).
Purified gDNA was fragmented using a Covaris S2 Sonicator. Libraries were prepared with 10ug gDNA using the Ovation® Ultralow Methyl Seq DR Multiplex System 1-8, 9-16 (NuGen 0335 and 0336). Libraries were pooled and sequenced at 100PE on a HiSeq 2000 in standard run mode to a read depth of >180M mapped reads at the Harvard FAS core.

treatment_protocol: Direct cardiac reprogramming was performed on neonatal mouse cardiac fibroblasts as previously described (Ieda et al. 2010; Qian et al. 2013). Briefly, tissue explants from αMHC-GFP+ neonatal mouse hearts are cultured for ~10 days, allowing expansion of fibroblast population. Thy1+/αMHC-GFP- cells, largely fibroblasts, are isolated by fluorescence-activated cell sorting (FACS), infected with freshly prepared Gata4, Mef2c, and Tbx5 (GMT) retroviruses or a dsRed control retrovirus, and cultured with Tgfβ and Wnt inhibitors (sb431542 and xav939, respectively; Mohamed et al. 2017) prior to FACS harvest of αMHC-GFP+ or dsRed+ cells at time points following reprogramming initiation. We completed three biological replicates per condition.

tag: strain

value: alphaMHC-GFP

tag: exogenous retroviral expression

value: Gata4, Mef2c, Tbx5

tag: chemical treatment

tag: reprogramming time point

value: Day 7

value: alphaMHC-GFP+ sorted induced cardiomyocytes


title: NS_WGBS_iCM_Day3_rep2

description:
BC5
all.bsseq.matrix.txt.minustwocols.gz
all.dmr.Day3.txt
all.dmr.Day3.annotated.txt

value: Day 3


title: NS_WGBS_iCM_Day3_rep3

description:
BC6
all.bsseq.matrix.txt.minustwocols.gz
all.dmr.Day3.txt
all.dmr.Day3.annotated.txt


title: Plasmsablasts_Mouse2

description: Sample name: 2


title: NS_WGBS_Fibroblast_rep3

description:
BC3
all.bsseq.matrix.txt.minustwocols.gz

value: dsRed

value: dsRed+ sorted fibroblasts (control infection)


title: NS_WGBS_Fibroblast_rep2

description:
BC2
all.bsseq.matrix.txt.minustwocols.gz


title: RNA160225TP_3_H21NA

value: High Drinker


title: RNA160225TP_38_L292NA

value: Male


title: RNA160225TP_29_L2123NA

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: Nucleus Slc32a1-Cre:H2BG Vg_A3

description:
SS2_16_033_Slc32a1_counts.txt
SS2_16_striatal_nuclei_counts.txt

value: untreated


title: RNA160225TP_27_L202NA

value: Low Drinker


title: Dam Only

first: Karen

last: Reddy

address: 855 North Wolfe Street

department: Center for Epigenetics/Biological Chemistry

institute: Johns Hopkins University

data_processing:
Library strategy: DamID-Seq
DamID-seq analysis—DamID-seq reads were processed using LADetector (available at https://github.com/thereddylab/LADetector)
Reads were quality trimmed using a sliding window quality score average over 3 bases and a minimum score cutoff of 30.
This was followed by trimming any matching overlap between read-ends and sequencing or DamID adaptor-primer sequence. Reads containing a DamID adaptor-primer sequence were split and adaptor-primer sequence removed.
All resulting reads greater than 20 bp were aligned to mm9 using Bowtie (Langmead et al., 2009) with parameters “—tryhard–best–m 1.” Unaligned reads had 13 bases trimmed from the 5′ end and remapped, and the resultant unmapped reads were trimmed 13 bases from the 3′ end and remapped. Total aligned reads were assigned to DpnI bins, with reads straddling bin boundaries counting toward both. Prior to scoring, a value of 0.5 was added to bins with no reads. Bins falling in unaligned regions were removed prior to analysis. DamID scores were calculated for all non-zero bins as the log2 ratio of Dam-POI over unfused Dam.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files named X.bed (eg LMNA.bed) include genomic coordinates and scores (log2 ratios) for each sample per Dpn bin.  Tab-delimited text files named X_LADs.bed (eg LMNA_LADs.bed) include genomic coordinates of LADs

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were cultured according to their established protocols, in medium containing DMEM High, 10% FBS, Penicillin/Streptomycin and L-glutamine.

extract_protocol:
MEFs were collected by trypsinization and DNA was isolated using QIAamp DNA Mini kit (Qiagen,  51304), followed by ethanol precipitation and resuspension to 1 µg/ul in 10 mM Tris, pH 8.0.  DamID was performed as described previously (L.Guelen et al, Nature 2008)
post-DamID amplified material was randomized  by performing an end repair reaction, followed by ligation and sonication.  Randomized fragments were subjected to sequencing library preparation with Illumina Paired End Sequencing Kit.

treatment_protocol: Cells were transduced with murine retroviruses harboring an expression cassette for either Dam-only, Dam-Lamin A or Dam-Lap2b and subsequently cultured in DMEM High, 10% FBS, Penicillin/Streptomycin and L-glutamine.

tag: group

value: Dam Only

value: Mouse Embryonic Fibroblasts

value: wild type


title: NS_WGBS_iCM_Day7_rep3

description:
BC9
all.bsseq.matrix.txt.minustwocols.gz
all.dmr.Day7.txt
all.dmr.Day7.annotated.txt

tag: genotype


title: NS_WGBS_iCM_Day7_rep1

description:
BC7
all.bsseq.matrix.txt.minustwocols.gz
all.dmr.Day7.txt
all.dmr.Day7.annotated.txt


title: RNA160225TP_26_L192NA


title: RNA160225TP_28_L211NA


title: Lap2b


title: RNA160225TP_25_L191NA


title: NS_WGBS_iCM_Day3_rep1

description:
BC4
all.bsseq.matrix.txt.minustwocols.gz
all.dmr.Day3.txt
all.dmr.Day3.annotated.txt


title: input DNA

city: odense

first: mads

last: thomassen

address: soender boulevard 29

country: Denmark

institute: odense university hospital

data_processing:
The 50-nt sequence reads were identified by Sequencing Service (using Illumina’s Hi-Seq)
ChIP-seq reads were aligned to the mm9 genome assembly using BWA algorithm with default settings
Peaks were called using MACS version 1.4.2
Peaks were filtered using following criteria to define a more stringent protein-DNA interactome: 1) the p-value cutoff was set to <10-6; 2) MACSMFold was set to 10,30; 3) MACSTagSize was set to 50
Genome_build: mm9
Supplementary_files_format_and_content: .txt-file containing the active regions identified in OPCs and Ols using MACS  version 1.4.2 and p<10e-6

source_name: Oligodendrocyte progenitor cells and oligodendrocytes (OPCs and Ols)

growth_protocol: Cells for ChIP-seq were all isolated and cultured at the same time in 8x T175 flasks in SATO serum-free media enriched with 2% B-27 (Invitrogen), 2% SM1 neuronal supplement (Stemcell Technologies), PDGF-AA (10 ng/mL) (315-17, PeproTech), NT-3 (1 ng/mL) (PeproTech), and CNTF (10 ng/mL) (PeproTech) until the flasks were relatively confluent.

extract_protocol:
Lysates were clarified from sonicated nuclei and Nkx2.2-DNA complexes were isolated with antibody. The ChIP-seq library was prepared by Active Motif, Carlsbad, CA, USA using FactorPath method (Active Motif)
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: The flasks were passaged into 2x 15cm dishes with 2.5 million OPCs, which were maintained in SATO serum-free media enriched with 2% B-27 (Invitrogen), 2% SM1 neuronal supplement (Stemcell Technologies), PDGF-AA (10 ng/mL) (315-17, PeproTech), NT-3 (1 ng/mL) (PeproTech), and CNTF (10 ng/mL) (PeproTech) for 2 more days before harvested as OPCs (10-20 million cells), or were passaged into 1x 15cm dishes with 20 million OPCs. These OPCs were differentiated into postmitotic Ols by PDGF_AA removal and addition of T3 (40 ng/mL) (Sigma-Aldrich) to the media for 48 hrs.

value: Proliferating OPC (1.5e7) isolated from enzymatically dissociated cortices of P7 mice using anti-PDGFRA antibody and ex vivo differentiated Ols

tag: chip antibody


title: Nkx2.2_Ol_ChIPSeq

source_name: Oligodendrocytes (Ols)

value: Ex vivo differentiated Ol (1.5e7) from cortices of P7 mice

value: Anti-Nkx2.2 monoclonal antibody (Protein G affinity purified supernatant from hybridomas (74.5A5-b) developed by Prof. Thomas M Jessell, Columbia University, USA, and obtained from Developmental Studies Hybridoma Bank, University of Iowa, USA).


title: RNA160225TP_24_H181NA


title: Nkx2.2_OPC_ChIPSeq

source_name: Oligodendrocyte progenitor cells (OPCs)

value: Proliferating OPC (1.5e7) isolated from enzymatically dissociated cortices of P7 mice using anti-PDGFRA antibody


title: RNA160225TP_47_L361NA


title: LMNA

value: Dam-Lamin A


title: RNA160225TP_2_H12NA


title: RNA160225TP_20_H152NA


title: RNA160225TP_23_H171NA


title: RNA160225TP_21_H153NA


title: RNA160225TP_22_H161NA


title: RNA160225TP_19_H141NA


title: Stroma rich area in trastuzumab administrated PDX tumor_3

city: Fukuoka

first: Ryosuke

last: Matsukane

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Pharmacy

institute: Kysuhu University Hospital

description: Trastuzumab B3

hyb_protocol: 600 ng of Cy3-labelled cRNA hybridized to Agilent SurePrint G3 Human GE Microarrays 8x60K Ver3.0 for 17 hours at 65°C,  in a rotating (10 rpm) DNA Microarray Hybridization Oven. After hybridization, microarrays were washed by Gene Expression Wash Pack (Agilent).

scan_protocol: Slides were scanned immediately after washing on the DNA Microarray Scanner (Agilent) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software Ver. 10.7.1.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 10 ng total RNA using Low Input Quick Amp Labeling Kit (Agilent) followed by cRNA amplification.  Dye incorporation and cRNA amplification yield were checked with the NanoDrop One  and confirmed all samples were showed values higher than reference ( more than 15x amplification and 6 pmol/µg dye incorporation).

growth_protocol: Patient tumor samples (3 x 3 mm) were transplanted to mammary fat pad of 4 week old female SCID-Beige and these patient derived tumor transplantation was defined as a first generation.When tumor size reached certain volume, mice were euthanized and extracted tumor were passaged into additional mice as a next generation. Second to fourth generation PDX were used in these experiments after evaluating tumor characteristics were not changed from the original patient tumor.

extract_protocol: After 24 hours of administration, PDX mouse was sacrificed and excised tumor was frozened immediately. Tumor tissues were sliced into serial sections by cryomicrotome and  two pattern of characteristic area were selected and cut off by Leica LMD 6500 from 8 µm thickness, 6 sequential tumor sections. RNA was extracted using RNeasy micro kit (QIAGEN, CA, USA) followed by manufacture’s protocol. To guarantee the RNA quality for microarray, concentration and RNA integrity number (RIN) was measured by Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA).

treatment_protocol: Normal saline (Control) or trastuzumab (10 mg/kg) was administrated intraperitoneally.

tag: gender source

value: female

value: NCC-BCP69 patient derived xenograft (PDX) tumor

tag: classification

value: invasive ductal carcinoma

tag: treatment

value: trastuzumab (10 mg/kg)

tag: tumor region

value: stroma rich area


title: Stroma rich area in trastuzumab administrated PDX tumor_2

description: Trastuzumab B2

tag: tissue


title: Stroma poor area in trastuzumab administrated PDX tumor_3

description: Trastuzumab A3

value: stroma poor area


title: 20 min sample vs. control 1 (2)

city: Katano shi

first: Moritoshi

last: Iino

state: Osaka Prefecture

address: Kisaichi

department: Graduate School of Science

institute: Osaka City University

description: 20 min after the onset of 10 min UV-B (vs. control 1), biological replicate 2

hyb_protocol: Each UV-B-treated sample (Cy5-labelled, 825 ng cRNA) was mixed with each of control 1 and 2 samples (Cy3-labelled, 825 ng cRNA); therefore, two mixtures were prepared for each UV-B-treated sample. The mixtures were applied to microarrays and hybridization was performed at 65oC for 17 h.

scan_protocol: Scanned with an Agilent Scanner G2505B Images were quantified using Agilent Feature Extraction Software (version 11.5.1.1)

data_processing: Agilent Feature Extraction Software (version 11.5.1.1) with default setting was used for background subtraction and LOWESS normalization

organism: Oryza sativa Japonica Group

source_name: coleoptiles

label_protocol: Two-color microarray analysis was performed with the Rice Expression 4x44K Microarray (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacture’s protocols. Control samples and UV-B-treated samples (400 ng RNA each) were labelled with Cy3 and Cy5, respectively, purified with an RNeasy Mini Kit (Qiagen GmbH, Hilden), and measured for cRNA concentration.

growth_protocol: Dehusked and surface-sterilized caryopses of japonica rice (cv. Nipponbare) were surface-sown on 0.7% agar in 4.5-mL acrylic cuvettes. Sown caryopses (one caryopsis per cuvette) were placed inside boxes made of transparent red acrylic and cultured at 25±1°C under red light (2.5-3.0 μmol m-2 s-1 at the plant position). Inside the boxes was maintained at high humidity with wet paper towel placed on the bottom. Sown caryopses were cultured for three days and used for experiments when the length of their coleoptiles reached 3-4 mm (approximately half of the final mean length achieved under the red light growth condition).

extract_protocol: Each frozen coleoptile sample (30-40 mg FW) was ground to a fine powder with a mortar and pestle in liquid N2. Total RNA was extracted with the RNeasy Plant Mini Kit (Qiagen GmbH, Hilden, Germany) following the manufacturer’s protocol.

treatment_protocol: Coleoptiles of intact seedlings were irradiated bilaterally with UV-B for 10 min (total fluence rate: 0.065 μmol m-2 s-1) and harvested 20 and 60 min after the onset of irradiation (20- and 60-min samples, respectively). During and after UV-B treatment, seedlings were maintained under the red light use during seedling growth. Four coleoptiles were irradiated simultaneously and harvested within ±1 min of the scheduled incubation period, and this irradiation procedure was repeated at least twice to obtain eight coleoptiles per sample. Incubation after UV-B irradiation was terminated by harvesting each coleoptile (without enclosed leaves) and immediately freezing it in liquid N2, and the frozen coleoptiles were stored at -80oC. Non-treated controls (8 coleoptiles per sample) were prepared just before and after irradiation treatment (controls 1 and 2, respectively).

value: coleoptiles

tag: cultivar

value: Nipponbare

value: control 1

value: 20 min sample


title: Nucleus Slc32a1-Cre:H2BG Vg_B1

data_processing:
fastq files were aligned to mouse genome version mm10
 The alignments of reads towards the indicated genome assembly using SAMtools
The expression values were computed per gene as described in Ramsköld et al (2009 PLoS Comp Biol), using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo
Clustering and marker identification was done using the Seurat package in R (versions 1.4.0 and 2.3.2)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts per gene

source_name: Slc32a1-Cre nucleus striatum

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

tag: background strain

value: untreated


title: 20 min sample vs. control 2 (2)

description: 20 min after the onset of 10 min UV-B (vs. control 2), biological replicate 2

value: control 2


title: 20 min sample vs. control 2 (3)

description: 20 min after the onset of 10 min UV-B (vs. control 2), biological replicate 3


title: Stroma poor area in trastuzumab administrated PDX tumor_2

description: Trastuzumab A2


title: 20 min sample vs. control 1 (3)

description: 20 min after the onset of 10 min UV-B (vs. control 1), biological replicate 3


title: 60 min sample vs. control 1 (2)

description: 60 min after the onset of 10 min UV-B (vs. control 1), biological replicate 2

value: 60 min sample


title: Stroma poor area in trastuzumab administrated PDX tumor_1

description: Trastuzumab A1


title: 60 min sample vs. control 2 (2)

description: 60 min after the onset of 10 min UV-B (vs. control 2), biological replicate 2


title: Stroma rich area in control PDX tumor_3

description: Control B3

source_name: Stroma rich area in control PDX tumor

value: Normal saline (Control)


title: Stroma rich area in control PDX tumor_1

description: Control B1


title: Stroma rich area in control PDX tumor_2

description: Control B2


title: RNA160225TP_18_H131NA

data_processing:
FastQC was used for checking the quality of the raw sequence data.
Sequence data were then aligned using Spliced Transcripts Alignment to a Reference (STAR; Dobin et al., 2013), allowing for a maximum of 3 mismatches per 100 bp read. Reads were uniquely aligned greater than 88%, for all samples.
Reads were mapped to known genomic features to generate counts at the gene level using FeatureCounts (SubRead package).
Gene expression data were imported into R and an upper-quartile normalization was performed using edgeR (in R). Inclusion in the network analysis required a gene read density threshold of an average of greater than 1 count per million (CPM).
Network connectivity for coexpression and cosplicing were calculated
Genome_build: Mus musculus (mm10)
Supplementary_files_format_and_content: obtained with featureCounts from the package SubRead

extract_protocol:
Mice were euthanized by cervical dislocation and then immediately decapitated. The brain was removed using RNase free tools, rinsed in cold saline, and then the regions of interest were dissected out using RNase free tools and an aluminum dissection stage. The dissected regions were placed independently into RNase-free microcentrifuge tubes containing TRIzol (Life Science Technologies, Carlsbad, CA, USA) and immediately frozen on dry ice. Samples were stored at -80°C for no longer than 1 month prior to RNA extraction. The prefrontal cortex (PFC) was removed as the medial third of a 1.5-mm slice from the anterior part of the brain just behind the olfactory bulbs. The next 1.4-mm slice included the nucleus accumbens (NAc), which was taken using a micropunch fashioned from a 16-gauge blunt cut needle; the anterior commissure was used as a landmark. Next, using the superior colliculus as a landmark, the most anterior portion of the brain was removed and discarded, and the next 1-mm slice was taken, from which the ventral midbrain (VMB) was obtained. This included the remaining tissue after the ventral third of that slice and the cerebral cortex were removed. Total RNA was isolated from dissected tissue with TRIzol, using a modified single-step acid guanidinium thiocyanate-phenol-chloroform extraction method (Chomczynski and Sacchi, 1987[23]). The extracted RNA was purified using a RNAeasy kit (Qiagen, Velencia, VA USA), with RNA purity and concentration determined by NanoDrop spectrophotometry (ND-1000, Thermo Scientific, Wilmington, DE, USA). All samples submitted to the Massively Parallel Sequencing Shared Resource (MPSSR) for processing met criteria of 260/280 nm absorption ratio greater than 1.8 and greater than 100 ng of total RNA. Within the MPSSR, an RNA Integrity Number (RIN) was generated for each sample, using a Caliper LabChip GX, with an inclusion criterion of RIN > 9 for library formation. A total of 144 samples were included, 24 per line per brain region.
Library formation (polyA+, stranded) and sequencing were performed according to Illumina’s specifications at the MPSSR. Libraries were multiplexed, 4 per lane, yielding approximately 50 million total reads per sample

tag: Sex

value: Male

tag: selected line

value: High Drinker

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: 60 min sample vs. control 1 (3)

description: 60 min after the onset of 10 min UV-B (vs. control 1), biological replicate 3


title: Stroma rich area in trastuzumab administrated PDX tumor_1

description: Trastuzumab B1

value: female


title: RNA160225TP_17_H121NA


title: 60 min sample vs. control 2 (3)

description: 60 min after the onset of 10 min UV-B (vs. control 2), biological replicate 3


title: RNA160225TP_16_H111NA


title: 20 min sample vs. control 2 (1)

description: 20 min after the onset of 10 min UV-B (vs. control 2), biological replicate 1


title: RNA160225TP_14_H102NA


title: Leaf_control_Line22_rep1

city: Guelph

first: JOSE

middle: A

last: CASARETTO

state: ON

address: 50 Stone Road E

department: MCB

country: Canada

institute: University of Guelph

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to 4x44K Rice Gene Expression Microarray for 16 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed with Wash Buffer 1 (Agilent) for 1 minute at room temperature followed by another wash with Wash buffer 2 (Agilent) for 1 minute, then dried by centrifugation. (Service provided by ImaGenes GmbH, Berlin, Germany).

scan_protocol: Microarray slides were scanned on a Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan resolution 10 um, Dye channel is set to Green and Green PMT is set to 100%). (Service provided by ImaGenes GmbH, Berlin, Germany).

data_processing: Scanned images were analyzed with the Feature Extraction Software 9.0 (Agilent) using default parameters to obtain background subtracted plus the spatially detrended processed signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. (Service provided by ImaGenes GmbH, Berlin, Germany).

organism: Oryza sativa

source_name: leaf, transgenic line 22

label_protocol: Cy3-labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. (Service provided by ImaGenes GmbH, Berlin, Germany).

growth_protocol: Plants were grown in 1-L pots with an inert mix of clay:vermiculite (1:1) as substrate and fertilized with nutrient solution. Plants were grown in chambers in a 16 h daylight photoperiod and at a 30°C/20°C day/night cycle.

extract_protocol: Extraction of total RNA from leaves was carried out with the TRIZOL® method (Invitrogen) following the manufacturer's recommendations and then treated with RNase-free DNase I (Ambion). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: No treatment prior RNA extraction

value: leaf


title: 20 min sample vs. control 1 (1)

description: 20 min after the onset of 10 min UV-B (vs. control 1), biological replicate 1


title: 60 min sample vs. control 1 (1)

description: 60 min after the onset of 10 min UV-B (vs. control 1), biological replicate 1


title: Stroma poor area in control PDX tumor_3

description: Control A3

source_name: Stroma poor area in control PDX tumor

value: NCC-BCP69 patient derived xenograft (PDX) tumor

value: invasive ductal carcinoma


title: RNA160225TP_15_H103NA


title: 60 min sample vs. control 2 (1)

description: 60 min after the onset of 10 min UV-B (vs. control 2), biological replicate 1


title: PDGF-AB-treated rep2 - small colony - passage 5

city: Westmead

first: Ashley

last: Waardenberg

state: NSW

address: 214 Hawkesbury Road

country: Australia

institute: Children's Medical Research Institute

hyb_protocol: 3.52 ug of fragmented labelled ssDNA was hybridised to Mouse Gene 1.0 ST Gene Arrays  for 16 hours at 45°C in the Affymetrix GeneChip Oven. Arrays were washed on the Affymetrix Fluidics 450 instrument as per manufacturer’s protocol using the Affymetrix GeneChip Hybridization Wash & Stain kit for cartridge arrays.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip 3000 7G Scanner instrument as per manufacturer’s protocol

data_processing: Affymetrix GeneChip Command Console (AGCC) software was used to generate the CEL files from the DAT image files. All analyses were performed in R, using the affy, affyPLM and limma libraries. Data were Robust Multichip Average (RMA) normalised.

source_name: SMALL Passage 5 cardiac colony forming units - fibroblast (cCFU-F), PDGF-AB treated

label_protocol: 100ng of total RNA was labelled using the Affymetrix WT kit (Ambion).

growth_protocol: Primary cells were isolated from the Bl6 mice and cultured at 37oC and 5% CO2.

extract_protocol: Total RNA was extracted using RNAeasy micro RNA isolation kit (Qiagen) and the quality of RNA was assessed using the Nanodrop (Thermofisher Scientific; 230/260>1.8, 260/280>1.8) and Bioanalyzer (Agilent, RIN>8.0). The RNA was then sent to the Ramaciotti Center for Genomics (University of New South Wales, Sydney) for further processing.

treatment_protocol: Cultured cells were treated with 1um/10uM of AG1296, PDGF-AB (50ng/ml) or untreated.

tag: age

value: 12 weeks

value: male

tag: cell type

tag: isolated cardiac cells

value: SCA1+PDGFRα+CD31- (S+P+)

tag: colony size

value: small

tag: passage

value: passage 5


title: PDGF-AB-treated rep1 - small colony - passage 15

source_name: SMALL Passage 15 cardiac colony forming units - fibroblast (cCFU-F), PDGF-AB treated

tag: strain

value: passage 15


title: Untreated control rep3 - small colony - passage 5

source_name: SMALL Passage 5 cardiac colony forming units - fibroblast (cCFU-F), UNTREATED


title: HBL-1-Res-C

city: columbus

first: Lalit

last: Sehgal

state: Ohio

department: Hematology

institute: The Ohio State University

description: Gene expression after acquired resistance to Ibrutinib (8months)

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers. The labeled cRNAs were hybridized onto the Whole Human Genome Oligo Microarray (4 x 44K, Agilent Technologies). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

scan_protocol: After washing, slides were scanned with the Agilent DNA Microarray Scanner. Data was extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX 12.1 software. Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies). After quantile normalization of the raw data, genes that at least 3 out of 24 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering and Volcano filtering. Pathway analysis and GO Analysis were applied to determine the roles of these differentially expressed genes played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable gene expression profiling among samples.Further data analysis was performed using Agilent GeneSpring GX 12.1 software. To identify differentially expressed genes, we performed a Fold Change filtering between two samples and a Volcano Plot filtering between two groups. The default threshold is Fold Change>=2.0, P-value<=0.05.

source_name: cell line Ibrutinib resistant rep 3

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling. Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: Total RNA was isolated using Qiagen kits, following which Integrity and concentration of RNA was assessed after RNA extraction and prior to sample labeling.

treatment_protocol: The Cell lines were cultured at LD75 for over 8months and Ibrutinib resistant clones were selected and gene profiled.

tag: cell line

value: ABC-DLBCL

tag: drug (ibrutinib) sensitivity

value: Resistant


title: Leaf_control_Line32_rep1

source_name: leaf, transgenic line 32


title: PDGF-AB-treated rep1 - small colony - passage 5

value: cardiac colony forming units - fibroblast (cCFU-F)


title: PDGF-AB-treated rep3 - small colony - passage 5


title: PDGF-AB-treated rep2 - small colony - passage 15


title: Stroma poor area in control PDX tumor_1

description: Control A1

tag: gender source

value: Normal saline (Control)

value: stroma poor area


title: PDGF-AB-treated rep3 - small colony - passage 15


title: RNA160225TP_13_H101NA

city: Portland

first: Priscila

last: Darakjian

address: 3181 SW Sam Jackson Park Road, L470

institute: Oregon Health and Science University

source_name: High Drinker_Nucleus Accumbens

treatment_protocol: For the RNA-Seq analysis, we obtained brain tissue from experimentally naïve, non-MA exposed replicate 3 high and low line mice from second or later litters of generation S5. Animals were 60 - 86 days of age at the time of tissue harvesting (mean ± SEM = 69 ± 1 d). On the day of tissue harvesting, the group-housed male mice (2-3 per cage) were moved from the colony room, 4 h prior to tissue collection to allow them to acclimate to the procedure room environment. Sex has not impacted the response to selection for MA intake (Shabani et al., 2011[22]; Wheeler et al., 2009[10]), and male mice were used in our previous gene expression array studies (Shabani et al., 2011; Belknap et al., 2013[11]). Dissection occurred between 1100 and 1300 h.

value: Male

value: High Drinker


title: HBL-1-Res-B

source_name: cell line Ibrutinib resistant rep 2


title: Stroma poor area in control PDX tumor_2

description: Control A2

value: female

tag: classification


title: OCI-LY-10-Res-C


title: Untreated control rep1 - small colony - passage 5


title: Untreated control rep2 - small colony - passage 5


title: RNA160225TP_12_H91NA

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: HBL-1-Res-A

source_name: cell line Ibrutinib resistant rep 1


title: RNA160225TP_11_H82NA


title: Untreated control rep3 - large colony - passage 15

source_name: LARGE Passage 15 cardiac colony forming units - fibroblast (cCFU-F), UNTREATED

value: large


title: RNA160225TP_1_H11NA


title: NS_WGBS_Fibroblast_rep1

description:
BC1
all.bsseq.matrix.txt.minustwocols.gz

source_name: neonatal mouse heart

tag: genotype

value: alphaMHC-GFP

tag: exogenous retroviral expression

value: dsRed

tag: chemical treatment

tag: reprogramming time point

value: Day 7

value: dsRed+ sorted fibroblasts (control infection)


title: RNA160225TP_10_H72NA

tag: tissue


title: Untreated control rep2 - large colony - passage 15

value: 12 weeks

tag: Sex

value: male

value: SCA1+PDGFRα+CD31- (S+P+)


title: OCI-LY-10-Res-B

value: ABC-DLBCL


title: OCI-LY-10-Res-A

value: Resistant


title: D6 undifferentiated

source_name: brown adipose tissue

tag: strain/background

value: immortalised brown adipose cells

tag: developmental stage

value: undifferentiated

tag: passage number


title: Untreated control rep3 - large colony - passage 5

source_name: LARGE Passage 5 cardiac colony forming units - fibroblast (cCFU-F), UNTREATED

tag: age

tag: cell type

tag: isolated cardiac cells

value: passage 5


title: D5 undifferentiated


title: Untreated control rep1 - large colony - passage 15

tag: strain

value: cardiac colony forming units - fibroblast (cCFU-F)

tag: colony size

tag: passage

value: passage 15


title: Untreated control rep2

description:
Untreated_control_Rep2
Gene expression data from cCFU-Fs Untreated

tag: treated with

value: none (untreated)


title: Untreated control rep1 - large colony - passage 5


title: Untreated control rep2 - large colony - passage 5


title: PDGF-AB-treated rep3

description:
PDGF_Rep3
Gene expression data from cCFU-Fs treated with PDGF-AB

source_name: cCFU-F_PDGF-AB treated

value: PDGF-AB


title: OCI-LY1-Res-C

tag: cell line

value: GC-DLBCL

tag: drug (ibrutinib) sensitivity


title: OCI-LY1-Res-B


title: HBL-1-C

description: Gene expression Parental

source_name: cell line parental rep 3

value: Sensitive


title: Untreated control rep3

description:
Untreated_control_Rep3
Gene expression data from cCFU-Fs Untreated


title: AG1296-10uM-treated rep3

description:
AG1296_10M_Rep3
Gene expression data from cCFU-Fs treated with 10uM AG1296

source_name: cCFU-F_AG1296 treated with 10uM


title: PDGF-AB-treated rep1

description:
PDGF_Rep1
Gene expression data from cCFU-Fs treated with PDGF-AB


title: PDGF-AB-treated rep2

description:
PDGF_Rep2
Gene expression data from cCFU-Fs treated with PDGF-AB


title: C2 undifferentiated


title: B6 undifferentiated


title: AG1296-10uM-treated rep1

description:
AG1296_10M_Rep1
Gene expression data from cCFU-Fs treated with 10uM AG1296


title: HBL-1-B

description: Gene expression Parental

source_name: cell line parental rep 2


title: OCI-LY1-B

description: Gene expression Parental


title: Untreated control rep1

description:
Untreated_control_Rep1
Gene expression data from cCFU-Fs Untreated


title: 5Pi_cZ_R2

city: Pozuelo de Alracon

first: Juan

middle: Carlos

last: del Pozo

state: Madrid

address: Campus de Montegancedo, UPM

department: Biotechnology

country: Spain

institute: Centro de Biotecnología y Genómica de Plantas

description: grown without phosphate and treated with cis-zeatin

data_processing:
Basecalls performed using CASAVA version 1.4
Clean (FastQC software (Babraham-Bioinformatics, 2014).  Reads are mapped to a reference sequences using HISAT2 with 8 mismatches allowed.
Reads count to a reference  genome  (TAIR 42.gff3) using the htseq-count tool.
Differential expression analysis was calculated with edgeR with the following parameters: FDR<0.05, fold change >2 fold  or   < -2 fold
Genome_build: Atabidopsis thaliannTAIR 10
Supplementary_files_format_and_content: tab-delimited text files including normalized counts.

organism: Arabidopsis thaliana

source_name: roots

growth_protocol: Arabidopsis thalinaan (Col-0) seedlings were grown  in Murashige and Skoog medium containing 625 or 5 µM of phosphate for 8 days  and then treated with 5 µM of cis-zeatin or trans-zeatin fro 8 hours.

extract_protocol:
Total  RNA was isolated from Arabidopsis plants using the Trizol reagent and RNeasy columns (Qiagen). Quantity and quality measurements were taken using a NanoDrop spectrophotometer and Bioanalyzer.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized  using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short  fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent  2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using  Illumina HiSeqTM 2000 or other sequencer when necessary
polyA library

tag: ecotype

value: Columbia

tag: treatment


title: B5 undifferentiated


title: OCI-LY1-A

description: Gene expression Parental

source_name: cell line parental rep 1


title: 5Pi_cZ_R1

value: grown without phosphate and treated with cis-zeatin


title: B4 undifferentiated


title: AG1296-1uM-treated rep3

description:
AG1296_1M_Rep3
Gene expression data from cCFU-Fs treated with 1uM AG1296

source_name: cCFU-F_AG1296 treated with 1uM


title: 5Pi_cZ_R3


title: D4 undifferentiated


title: 5Pi_tZ_R3

description: grown withoutout phosphate and treated with trans-zeatin

value: grown without phosphate and treated with trans-zeatin


title: OCI-LY1-Res-A


title: B1 undifferentiated


title: B3 undifferentiated


title: 5Pi_tZ_R2

description: grown without phosphate and treated with trans-zeatin


title: C3 undifferentiated


title: C4 undifferentiated


title: D3 undifferentiated


title: 5Pi_R3

description: grown without phosphate

value: grown without phosphate


title: 5Pi_R2

description: grown without phosphate


title: A5 undifferentiated


title: A6 undifferentiated


title: A3 undifferentiated


title: A2 undifferentiated


title: 5Pi_R1

description: grown without phosphate


title: 5Pi_tZ_R1

description: grown without phosphate and treated witht trans-zeatin


title: Pi_cZ_R2

description: grown with phosphate and treated with cis-zeatin


title: Pi_cZ_R3

value: grown with phosphate and treated with cis-zeatin


title: Pi_cZ_R1


title: Pi_tZ_R3

description: grown with phosphate and treated with trans-zeatin


title: Pi_tZ_R2

value: grown with phosphate and treated with trans-zeatin


title: Pi_R3

description: grown with phosphate

value: grown with phosphate


title: Pi_R1

description: grown with phosphate


title: Pi_R2

description: grown with phosphate